Main Indicators
In order to partition networks into components or clusters, we deploy a community detection technique based on the Lovain Algorithm (Blondel et al., 2008). The Lovain Algorithm is a heuristic method that attempts to optimize the modularity of communities within a network by maximizing within- and minimizing between-community connectivity. We identify the following communities = knowledge bases.
| com | name | dgr_int | dgr |
|---|---|---|---|
| Knowledge Base 1: KB 1 | |||
| 1 | RAPOSO G. STOORVOGEL W. EXTRACELLULAR VESICLES: EXOSOMES MICROVESICLES AND FRIENDS (2013) | 16828 | 17297 |
| 1 | VALADI H. EKSTROM K. BOSSIOS A. SJOSTRAND M. LEE J.J. LOTVALL J.O. EXOSOME-MEDIATED TRANSFER OF MRNAS AND MICRORNAS IS A NOVEL MECHANISM OF GENETIC… | 9851 | 10011 |
| 1 | TRAJKOVIC K. HSU C. CHIANTIA S. RAJENDRAN L. WENZEL D. WIELAND F. SCHWILLE P. SIMONS M. CERAMIDE TRIGGERS BUDDING OF EXOSOME VESICLES INTO MULTIVES… | 8374 | 8446 |
| 1 | VALADI H. EKSTRÖM K. BOSSIOS A. SJÖSTRAND M. LEE J.J. LÖTVALL J.O. EXOSOME-MEDIATED TRANSFER OF MRNAS AND MICRORNAS IS A NOVEL MECHANISM OF GENETIC… | 7018 | 7106 |
| 1 | COLOMBO M. RAPOSO G. THERY C. BIOGENESIS SECRETION AND INTERCELLULAR INTERACTIONS OF EXOSOMES AND OTHER EXTRACELLULAR VESICLES (2014) | 6392 | 6559 |
| 1 | TAYLOR D.D. GERCEL-TAYLOR C. MICRORNA SIGNATURES OF TUMOR-DERIVED EXOSOMES AS DIAGNOSTIC BIOMARKERS OF OVARIAN CANCER (2008) | 6004 | 6078 |
| 1 | RAPOSO G. NIJMAN H.W. STOORVOGEL W. LIEJENDEKKER R. HARDING C.V. MELIEF C.J. GEUZE H.J. B LYMPHOCYTES SECRETE ANTIGEN-PRESENTING VESICLES (1996) | 5666 | 5723 |
| 1 | JOHNSTONE R.M. ADAM M. HAMMOND J.R. ORR L. TURBIDE C. VESICLE FORMATION DURING RETICULOCYTE MATURATION. ASSOCIATION OF PLASMA MEMBRANE ACTIVITIES W… | 5486 | 5543 |
| 1 | ROBBINS P.D. MORELLI A.E. REGULATION OF IMMUNE RESPONSES BY EXTRACELLULAR VESICLES (2014) | 4867 | 5016 |
| 1 | HOOD J.L. SAN R.S. WICKLINE S.A. EXOSOMES RELEASED BY MELANOMA CELLS PREPARE SENTINEL LYMPH NODES FOR TUMOR METASTASIS (2011) | 4790 | 4935 |
| Knowledge Base 2: KB 2 | |||
| 2 | COX J. MANN M. MAXQUANT ENABLES HIGH PEPTIDE IDENTIFICATION RATES INDIVIDUALIZED P.P.B.-RANGE MASS ACCURACIES AND PROTEOME-WIDE PROTEIN QUANTIFICAT… | 9462 | 9646 |
| 2 | COX J. NEUHAUSER N. MICHALSKI A. SCHELTEMA R.A. OLSEN J.V. MANN M. ANDROMEDA: A PEPTIDE SEARCH ENGINE INTEGRATED INTO THE MAXQUANT ENVIRONMENT (2011) | 3788 | 3809 |
| 2 | COX J. HEIN M.Y. LUBER C.A. PARON I. NAGARAJ N. MANN M. ACCURATE PROTEOME-WIDE LABEL-FREE QUANTIFICATION BY DELAYED NORMALIZATION AND MAXIMAL PEPTI… | 3567 | 3595 |
| 2 | TYANOVA S. TEMU T. SINITCYN P. CARLSON A. HEIN M.Y. GEIGER T. MANN M. COX J. THE PERSEUS COMPUTATIONAL PLATFORM FOR COMPREHENSIVE ANALYSIS OF (PROTE) | 2626 | 2642 |
| 2 | RAPPSILBER J. MANN M. ISHIHAMA Y. PROTOCOL FOR MICRO-PURIFICATION ENRICHMENT PRE-FRACTIONATION AND STORAGE OF PEPTIDES FOR PROTEOMICS USING STAGETI… | 2422 | 2446 |
| 2 | PETERSON A.C. RUSSELL J.D. BAILEY D.J. WESTPHALL M.S. COON J.J. PARALLEL REACTION MONITORING FOR HIGH RESOLUTION AND HIGH MASS ACCURACY QUANTITATIV… | 2231 | 2242 |
| 2 | MACLEAN B. TOMAZELA D.M. SHULMAN N. CHAMBERS M. FINNEY G.L. FREWEN B. KERN R. MACCOSS M.J. SKYLINE: AN OPEN SOURCE DOCUMENT EDITOR FOR CREATING AND… | 2183 | 2189 |
| 2 | AEBERSOLD R. MANN M. MASS-SPECTROMETRIC EXPLORATION OF PROTEOME STRUCTURE AND FUNCTION (2016) | 1808 | 1814 |
| 2 | PICOTTI P. AEBERSOLD R. SELECTED REACTION MONITORING-BASED PROTEOMICS: WORKFLOWS POTENTIAL PITFALLS AND FUTURE DIRECTIONS (2012) | 1498 | 1507 |
| 2 | LANGE V. PICOTTI P. DOMON B. AEBERSOLD R. SELECTED REACTION MONITORING FOR QUANTITATIVE PROTEOMICS: A TUTORIAL (2008) | 1427 | 1432 |
| Knowledge Base 3: KB 3 | |||
| 3 | HANAHAN D. WEINBERG R.A. HALLMARKS OF CANCER: THE NEXT GENERATION (2011) | 3354 | 9690 |
| 3 | PARDOLL D.M. THE BLOCKADE OF IMMUNE CHECKPOINTS IN CANCER IMMUNOTHERAPY (2012) | 1969 | 2544 |
| 3 | SHARMA P. ALLISON J.P. THE FUTURE OF IMMUNE CHECKPOINT THERAPY (2015) | 1553 | 1704 |
| 3 | TOPALIAN S.L. DRAKE C.G. PARDOLL D.M. IMMUNE CHECKPOINT BLOCKADE: A COMMON DENOMINATOR APPROACH TO CANCER THERAPY (2015) | 832 | 1099 |
| 3 | WILSON W.R. HAY M.P. TARGETING HYPOXIA IN CANCER THERAPY (2011) | 823 | 861 |
| 3 | KEIR M.E. BUTTE M.J. FREEMAN G.J. SHARPE A.H. PD-1 AND ITS LIGANDS IN TOLERANCE AND IMMUNITY (2008) | 816 | 867 |
| 3 | BARSOUM I.B. SMALLWOOD C.A. SIEMENS D.R. GRAHAM C.H. A MECHANISM OF HYPOXIA-MEDIATED ESCAPE FROM ADAPTIVE IMMUNITY IN CANCER CELLS (2014) | 714 | 729 |
| 3 | CHEN J. JIANG C.C. JIN L. ZHANG X.D. REGULATION OF PD-L1: A NOVEL ROLE OF PRO-SURVIVAL SIGNALLING IN CANCER (2016) | 674 | 674 |
| 3 | QUAIL D.F. JOYCE J.A. MICROENVIRONMENTAL REGULATION OF TUMOR PROGRESSION AND METASTASIS (2013) | 668 | 2138 |
| 3 | ISHIDA Y. AGATA Y. SHIBAHARA K. HONJO T. INDUCED EXPRESSION OF PD-1 A NOVEL MEMBER OF THE IMMUNOGLOBULIN GENE SUPERFAMILY UPON PROGRAMMED CELL DEAT… | 537 | 554 |
| Knowledge Base 4: KB 4 | |||
| 4 | LEVY J.M.M. TOWERS C.G. THORBURN A. TARGETING AUTOPHAGY IN CANCER (2017) | 3527 | 3622 |
| 4 | WHITE E. DECONVOLUTING THE CONTEXT-DEPENDENT ROLE FOR AUTOPHAGY IN CANCER (2012) | 2776 | 2841 |
| 4 | WHITE E. THE ROLE FOR AUTOPHAGY IN CANCER (2015) | 2414 | 2478 |
| 4 | YUE Z. JIN S. YANG C. LEVINE A.J. HEINTZ N. BECLIN 1 AN AUTOPHAGY GENE ESSENTIAL FOR EARLY EMBRYONIC DEVELOPMENT IS A HAPLOINSUFFICIENT TUMOR SUPPR… | 1886 | 1905 |
| 4 | LIANG X.H. JACKSON S. SEAMAN M. BROWN K. KEMPKES B. HIBSHOOSH H. LEVINE B. INDUCTION OF AUTOPHAGY AND INHIBITION OF TUMORIGENESIS BY BECLIN 1 (1999) | 1811 | 1826 |
| 4 | AMARAVADI R. KIMMELMAN A.C. WHITE E. RECENT INSIGHTS INTO THE FUNCTION OF AUTOPHAGY IN CANCER (2016) | 1786 | 1804 |
| 4 | KIMMELMAN A.C. WHITE E. AUTOPHAGY AND TUMOR METABOLISM (2017) | 1768 | 1791 |
| 4 | KIM J. KUNDU M. VIOLLET B. GUAN K.L. AMPK AND MTOR REGULATE AUTOPHAGY THROUGH DIRECT PHOSPHORYLATION OF ULK1 (2011) | 1762 | 1786 |
| 4 | MIZUSHIMA N. KOMATSU M. AUTOPHAGY: RENOVATION OF CELLS AND TISSUES (2011) | 1723 | 1748 |
| 4 | MIZUSHIMA N. YOSHIMORI T. OHSUMI Y. THE ROLE OF ATG PROTEINS IN AUTOPHAGOSOME FORMATION (2011) | 1570 | 1583 |
| Knowledge Base 5: KB 5 | |||
| 5 | VERHAAK R.G. HOADLEY K.A. PURDOM E. WANG V. QI Y. WILKERSON M.D. MILLER C.R. MESIROV J.P. INTEGRATED GENOMIC ANALYSIS IDENTIFIES CLINICALLY RELEVAN… | 2238 | 2327 |
| 5 | COMPREHENSIVE GENOMIC CHARACTERIZATION DEFINES HUMAN GLIOBLASTOMA GENES AND CORE PATHWAYS (2008) | 2146 | 2324 |
| 5 | LOUIS D.N. PERRY A. REIFENBERGER G. VON DEIMLING A. FIGARELLA-BRANGER D. CAVENEE W.K. OHGAKI H. ELLISON D.W. THE 2016 WORLD HEALTH ORGANIZATION CLA… | 1895 | 2030 |
| 5 | PATEL A.P. TIROSH I. TROMBETTA J.J. SHALEK A.K. GILLESPIE S.M. WAKIMOTO H. CAHILL D.P. MARTUZA R.L. SINGLE-CELL RNA-SEQ HIGHLIGHTS INTRATUMORAL HET… | 1589 | 1703 |
| 5 | BRENNAN C.W. THE SOMATIC GENOMIC LANDSCAPE OF GLIOBLASTOMA (2013) | 1338 | 1447 |
| 5 | BRENNAN C.W. VERHAAK R.G. MCKENNA A. CAMPOS B. NOUSHMEHR H. SALAMA S.R. ZHENG S. BERMAN S.H. THE SOMATIC GENOMIC LANDSCAPE OF GLIOBLASTOMA (2013) | 1211 | 1277 |
| 5 | STUPP R. MASON W.P. VAN DEN BENT M.J. WELLER M. FISHER B. TAPHOORN M.J. BELANGER K. BOGDAHN U. RADIOTHERAPY PLUS CONCOMITANT AND ADJUVANT TEMOZOLOM… | 1189 | 1282 |
| 5 | VERHAAK R.G. INTEGRATED GENOMIC ANALYSIS IDENTIFIES CLINICALLY RELEVANT SUBTYPES OF GLIOBLASTOMA CHARACTERIZED BY ABNORMALITIES IN PDGFRA IDH1 EGFR… | 1147 | 1234 |
| 5 | PATEL A.P. SINGLE-CELL RNA-SEQ HIGHLIGHTS INTRATUMORAL HETEROGENEITY IN PRIMARY GLIOBLASTOMA (2014) | 1141 | 1215 |
| 5 | BAO S. WU Q. MCLENDON R.E. HAO Y. SHI Q. HJELMELAND A.B. DEWHIRST M.W. RICH J.N. GLIOMA STEM CELLS PROMOTE RADIORESISTANCE BY PREFERENTIAL ACTIVATI… | 1113 | 1151 |
| Knowledge Base 6: KB 6 | |||
| 6 | KAUFMAN H.L. KOHLHAPP F.J. ZLOZA A. ONCOLYTIC VIRUSES: A NEW CLASS OF IMMUNOTHERAPY DRUGS (2015) | 3039 | 3383 |
| 6 | RUSSELL S.J. PENG K.W. BELL J.C. ONCOLYTIC VIROTHERAPY (2012) | 1889 | 2014 |
| 6 | LICHTY B.D. BREITBACH C.J. STOJDL D.F. BELL J.C. GOING VIRAL WITH CANCER IMMUNOTHERAPY (2014) | 1530 | 1712 |
| 6 | BOMMAREDDY P.K. SHETTIGAR M. KAUFMAN H.L. INTEGRATING ONCOLYTIC VIRUSES IN COMBINATION CANCER IMMUNOTHERAPY (2018) | 1201 | 1370 |
| 6 | KELLY E. RUSSELL S.J. HISTORY OF ONCOLYTIC VIRUSES: GENESIS TO GENETIC ENGINEERING (2007) | 1200 | 1271 |
| 6 | ANDTBACKA R.H. KAUFMAN H.L. COLLICHIO F. AMATRUDA T. SENZER N. CHESNEY J. DELMAN K.A. AGARWALA S.S. TALIMOGENE LAHERPAREPVEC IMPROVES DURABLE RESPO… | 1102 | 1182 |
| 6 | RIBAS A. DUMMER R. PUZANOV I. VANDERWALDE A. ANDTBACKA R.H.I. MICHIELIN O. OLSZANSKI A.J. FERNANDEZ E. ONCOLYTIC VIROTHERAPY PROMOTES INTRATUMORAL … | 998 | 1095 |
| 6 | ZAMARIN D. HOLMGAARD R.B. SUBUDHI S.K. PARK J.S. MANSOUR M. PALESE P. MERGHOUB T. ALLISON J.P. LOCALIZED ONCOLYTIC VIROTHERAPY OVERCOMES SYSTEMIC T… | 888 | 954 |
| 6 | KAUFMAN H.L. KIM D.W. DERAFFELE G. MITCHAM J. COFFIN R.S. KIM-SCHULZE S. LOCAL AND DISTANT IMMUNITY INDUCED BY INTRALESIONAL VACCINATION WITH AN ON… | 765 | 798 |
| 6 | LIU Z. RAVINDRANATHAN R. KALINSKI P. GUO Z.S. BARTLETT D.L. RATIONAL COMBINATION OF ONCOLYTIC VACCINIA VIRUS AND PD-L1 BLOCKADE WORKS SYNERGISTICAL… | 732 | 823 |